Saleem Shahzad, a 40-year-old father of three, vanished after leaving home in Islamabad to appear on a television talk show, two days after writing an article about links between rogue elements of the navy and Al-Qaeda.

Shahzad carved out a career writing about the plethora of Islamist militant networks operating in Pakistan, and warned human rights campaigners before his disappearance that he had been threatened by the Inter-Services Intelligence.

Shahzad’s body was found Tuesday, about 150 kilometres (93 miles) southeast of Islamabad. Police said it bore marks of torture.

“The cause of death is torture and there are several signs of torture on his body and face,” said Ashok Kumar, one of the doctors who carried out a post-mortem at Islamabad’s Pakistan Institute of Medical Science.

Another doctor told AFP that Shahzad’s lungs and liver had been damaged, that the body was swollen and bore more than 15 signs of having been beaten.

US Secretary of State Hillary Clinton condemned his murder and said his “reporting on terrorism and intelligence issues in Pakistan brought to light the troubles extremism poses to Pakistan’s stability”.

Wasim Fawad, a brother of Shahzad, told AFP that the family were in shock. His funeral was to take place in his home town of Karachi later Wednesday, after the body was flown from Islamabad.

“The post-mortem was being conducted on our request and we will also lodge a case with police. We want an investigation in this killing,” he said.

“My brother was killed for writing the truth. He paid a huge price, he sacrificed his life but always spoke the truth.”

Interior Minister Rehman Malik confirmed that a police investigation had been ordered and promised a reward of nearly $30,000.

“Anyone giving us information, evidence or clue about the murder will be given a reward of 2.5 million rupees ($29,410),” he told reporters.

But police officials in Islamabad and where the body was found each told AFP that the investigation was the responsibility of the other.

“Previous enquiries into the murders of journalists have not been made public and it is not clear if the fate of this enquiry would be any different,” the Pakistan Press Foundation said in a statement.

Reporters Without Borders says 16 journalists have now been killed since the start of 2010 in Pakistan, which it ranks 151st out of 178 countries in its press freedom index.

Shahzad worked for Italian news agency Adnkronos (AKI) and Asia Times Online, a news site registered in Hong Kong. After he vanished on Sunday, AKI said they feared he had been kidnapped.

In 2006, he was kidnapped by the Taliban in southern Afghanistan, accused of being a spy. He was set free after seven days.

Ali Dayan Hasan, senior South Asia researcher at Human Rights Watch, said Shahzad had complained about being threatened by the ISI and said his killing bore the hallmarks of the security services.

Last Friday, Shahzad published an investigative report in Asia Times Online that last week’s attack on a naval air base was carried out to avenge the arrest of naval officials arrested on suspicion of Al-Qaeda links.

The naval base attack began on May 22 and took 17 hours to repel. Officials said six militants destroyed two US-made surveillance aircraft and killed 10 security personnel in the standoff.

Prominent Pakistani investigative journalist Umar Cheema, who was abducted and tortured last year, said he believed that whoever picked up Shahzad had not meant to kill but to torture him to send a strong message to other journalists.

“It is really a very unfortunate incident. It breaks the myth that journalists in Pakistan, both local as well as foreign, are tolerated and work in a safe environment,” Cheema told AFP.